Filed by Bowne Pure Compliance





Exhibit 10.2




AMENDMENT NO. 1




TO




NOTE REPURCHASE AGREEMENT




This Amendment No. 1 to certain provisions of that Note Repurchase Agreement
dated as of July 1, 2008 by and between Alexandra Global Master Fund Ltd., a British Virgin
Islands International Business Company (“Holder”), on the one hand, and VaxGen, Inc., a Delaware
corporation (“Company”), on the other hand, is effective as of this 7th day of July, 2008 (the
“Amendment”).



Amendment of Note Repurchase Agreement




Whereas, the undersigned are parties to that certain Note Repurchase Agreement, dated
July 1, 2008 (the “Agreement”);



Whereas, the Holder and the Company wish to amend certain provisions of, and Schedule
A to, the Agreement; and



Whereas, pursuant to Section 5.6 of the Agreement, any term of the Agreement may be
amended, and the observance of any term of the Agreement waived (either generally or in a
particular instance and either retroactively or prospectively), by written consent of Holder and
the Company.




Now, Therefore, the undersigned agree as follows:



AGREEMENT




1. Amendment.




1.1 Section 1. Section 1 of the Agreement is hereby amended and restated
to read in its entirety as follows:



“1. Sale of Notes. Subject to the terms and conditions of this Agreement, the Company
agrees to purchase from the Holder, and the Holder agree to sell to the Company, the Notes
identified on Schedule A hereto, in the aggregate principal amount and for an aggregate
purchase price set forth on Schedule A hereto. The purchase and sale of the Notes shall
take place at one or more closings, at the time and place and on the dates indicated on
Schedule A hereto (which time and place are designated as the “Closing” and the dates
thereof each, a “Settlement Date”). At the Closing, the Holder shall deliver to the Company the
Notes, duly endorsed or accompanied by an assignment duly endorsed and in a form acceptable to the
Trustee, against payment of the aggregate purchase price described on Schedule A hereto
(the “Purchase Price”), by wire transfer in the amounts and using the wire transfer instructions to
be provided separately to the Company by Holder. Upon receipt by the Holder of the Purchase Price,
the Company shall become the legal and beneficial owner of the Notes and of all rights and interest
therein or related thereto and to the monies due and to become due under the terms
of the Notes. The Holder hereby agrees that upon receipt of the Purchase Price, the Notes shall be
cancelled and the Company shall have no further obligation to the Holder thereunder.”


 


 









 





1.2 Schedule A. Schedule A to the Agreement is hereby amended and restated to read
in its entirety as set forth on Exhibit A hereto.



2. Full Force and Effect. All other provisions of the Agreement shall remain in full force and
effect.



3. Construction. This Amendment shall be construed in accordance with the laws of the State of
New York, without regard to its choice of law provisions.



 [Remainder of page intentionally left blank.]




 


 









 







In Witness Whereof, the undersigned have executed this Amendment as of the
date set forth above.



	 	 	 	 	 	 	 
	ALEXANDRA GLOBAL MASTER
FUND LTD.	 	VAXGEN, INC.
	 
	 	 	 	 	 	 
	By: ALEXANDRA INVESTMENT	 	 	 	 
	MANAGEMENT, LLC, as	 	By:	 	/s/ James P. Panek
	 

	 	 	 	 	 	 
	Investment Advisor	 	 	 	Name: James P. Panek
	 

	 	 	 	 	 	Title: President and Chief Executive Officer
	 
	 	 	 	 	 	 
	By:

	 	/s/ Mikhail Filimonov	 	 	 	 
	 

	 	 	 	 	 	 
	 	 	Name: Mikhail Filimonov	 	Address for notices:
	 

	 	Title: Chairman and Chief Executive Officer	 	 	 	 
	 	 	 	 	VaxGen, Inc.
	 	 	 	 	349 Oyster Point Boulevard
	Address for notices:	 	South San Francisco, CA 94080
	 	 	 	 	Attn: Mr. James Panek
	Alexandra Global Master Fund Ltd.	 	Facsimile No.: (650) 624-4785
	c/o Alexandra Investment Management, LLC	 	 	 	 
	767 Third Avenue	 	 	 	 
	39th Floor	 	 	 	 
	New York, New York 10017	 	 	 	 
	 
	 	 	 	 	 	 
	Phone No: (212) 301-1800	 	 	 	 
	Facsimile No.: (212) 301-1810	 	 	 	 





 


 









 





Exhibit A




SCHEDULE A

to

Note Repurchase Agreement

dated as of July 1, 2008

by and between

ALEXANDRA GLOBAL MASTER FUND LTD.

and

VAXGEN, INC.




Title of Securities: 5 1/2% Convertible Senior Subordinated Notes due April 1 2010 (the “Notes” and
each, a “Note”)




			
	Aggregate Principal Amount of Note:	 	$7,500,000







			
	Purchase Price:	 	$6,150,000 ($820 for each $1,000 principal amount of Notes) plus accrued and unpaid
interest thereon to the Settlement Date.







			
	Accrued Interest:	 	$111,145.51 plus an additional $1,145.83 per day in the event that the Settlement
Date is extended to a later date by mutual agreement of the parties; provided, however, that the
parties hereby agree that if the Settlement Date is extended to a date later than July 8, 2008 as a
result of Holder being unable to deliver the applicable Note to the Company or its counsel on or
before the Closing on the Settlement Date, no additional interest shall accrue after such Settlement
Date with respect to such applicable Note.







			
	Aggregate Purchase Price:	 	$6,261,145.51 plus an additional $1,145.83 per day in the event that the
Settlement Date is extended to a later date by mutual agreement of the parties; provided, however,
that the parties hereby agree that if the Settlement Date is extended to a date later than July 8,
2008 as a result of Holder being unable to deliver the applicable Note to the Company or its counsel
on or before the Closing on the Settlement Date, no additional interest shall accrue after such
Settlement Date with respect to such applicable Note.







			
	Closing:	 	Offices of Cooley Godward Kronish, 3175 Hanover Street, Palo Alto, California 94304 at 9:00
A.M. (local time), on July 8, 2008 or such later date as Holder and the Company shall mutually
determine.







			
	Settlement Date:	 	July 8, 2008.







			
	Aggregate Principal Amount of Note:	 	$3,500,000







			
	Purchase Price:	 	$2,870,000 ($820 for each $1,000 principal amount of Notes) plus accrued and unpaid
interest thereon to the Settlement Date.







			
	Accrued Interest:	 	$51,867.84 plus an additional $534.72 per day in the event that the Settlement Date
is extended to a later date by mutual agreement of the parties; provided, however, that the parties
hereby agree that if the Settlement Date is extended to a date later than July 8, 2008 as a result of
Holder being unable to deliver the applicable Note to the Company or its counsel on or before the
Closing on the Settlement Date, no additional interest shall accrue after such Settlement Date with
respect to such applicable Note.







			
	Aggregate Purchase Price:	 	$2,921,867.84 plus an additional $534.72 per day in the event that the
Settlement Date is extended to a later date by mutual agreement of the parties; provided, however,
that the parties hereby agree that if the Settlement Date is extended to a date later than July 8,
2008 as a result of Holder being unable to deliver the applicable Note to the Company or its counsel
on or before the Closing on the Settlement Date, no additional interest shall accrue after such
Settlement Date with respect to such applicable Note.







			
	Closing:	 	Offices of Cooley Godward Kronish, 3175 Hanover Street, Palo Alto, California 94304 at 9:00
A.M. (local time), on July 8, 2008 or such later date as Holder and the Company shall mutually
determine.







			
	Settlement Date:	 	July 8, 2008, or such later date as Holder and the Company shall mutually determine.